The serious game I'm working on has many video and pdf files on top of the usual image & sound files.

Although these are sorted into directories in the project panel, when C2 exports to HTML5, only the images & sounds are placed in proper directories and all other files are just copied at the root.

Does anyone know if it is possible to customise C2 to have it create a structure under the /media directory which would be the same as the one you have in the project panel, e.g. /media/video and /media/pdf ?

This would probably be quite easy for Scirra to manage and would be useful for large projects if it's not currently possible.

It's not a major issue, but as there are many files, the organisation on the file server would be better if C2 copied them into specific directories, rather than copying them to the same location as the core files game files.

Yea, it would be nice, but if you keep it organized on your end, just trust that C2 will keep it organized inside the application.

Or if you are really OCD, you can load the files via the "Request URL" AJAX instead of using the "Request Project File". Then you can put the files wherever you want on your webserver and load them from there manually.

Or if you don't want to do that, you could try organizing them by file name, like group1-data1.json, group1-data2.json, group1-data1.json, group2-data2.json, etc.